Software Updates

cryoDRGN

a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

R

a free software environment for statistical computing and graphics.

ChimeraX

the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

SBGrid Installer

a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.13 - 10.15. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

MotionCor2

a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.

ModelAngelo

an automatic atomic model building program for cryo-EM maps.

PEET

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

ImageMagick

a software suite to create, edit, compose, or convert bitmap images.

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

ColabFold

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

OccuPy

a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and optionally also equalize the map according to occupancy while suppressing solvent amplification.

RELION Analyse Dashboard

a webapp to analyze in detail each RELION job in a given project.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

freesasa

a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) of biomolecules.

deepTools

a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

DiffDock

a state-of-the-art method for molecular docking

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

ChimeraX

the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

EMBuild

an automatic model building method of multi-chain protein complexes from intermediate-resolution cryo-EM maps, integrating AlphaFold structure prediction, FFT-based global fitting, domain-based semi-flexible refinement, and graph-based iterative assembling on the main-chain probability map predicted by a deep convolutional network.

crYOLO

a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.

PEET

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

EMAN2

a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.

Schrodinger

a suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.

OccuPy

a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and optionally also equalize the map according to occupancy while suppressing solvent amplification.

FFmpeg

a complete, cross-platform solution to record, convert and stream audio and video.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.